For the most part, the Pokémon series has cliche villains. If their plans of ruling the world or stealing a bunch of Pokémon are dissected even a little bit, it turns out to make no sense. However, that is often the case of villains written for shows, games, and comics that has children as its target audience.
At the same time, there are also villains who stand out from the crowd. Fans tend to like them more for various reasons. Sometimes it's because they are sympathetic, have an amusing personality, great character design, or even just due to the fact that they are nostalgic. Likable villains are always fun, and they are part of what makes the Pokémon series so special.
10 Giovanni
Giovanni is the classic Pokémon villain. He has been around since the beginning. By nostalgia alone, fans like him more than a lot of the other crime bosses in the series. His motivation is pretty simple, he just a greedy man who values wealth and power over compassion.
Some fans actually like Giovanni due to the many theories as to his true identity. Many have wondered if he is secretly Ash's father. In the manga, Pokémon Adventures, he is actually a more complex character who does have a son that he cares about.
9 Nobunaga
Nobunaga is the villain of Pokémon Conquest, a hidden gem that was released for the Nintendo DS in 2012. The game was basically Pokémon meets Fire Emblem.
Not only does Nobunaga have a cool character design, but his desire to conquer the region is fueled by the love he has for the people and Pokémon that live there. He hoped that by taking over the region, he could put an end to ceaseless battles. That ambition got out of hand and made him a villain for most of the game.
8 Archie
Archie is a bit of a joke to fans, and that is what has made him likable. His goal is a strange one: to cover the world in ocean. He hasn't really explained much as to why or for what purpose. A lot of fans joke that he just thinks it would be cool and once it happens, he will be like "Oops, I really did not think this through."
Most find him more interesting than the leader of Team Magma. He has more of a memorable personality and his character design is more fun and over-the-top.
7 The Rival In HeartGold & SoulSilver
In the Pokémon Adventures manga, the rival's name is Silver and he is actually the son of Giovanni. This is actually touched upon in the Soulsilver and Heartgold games. Due to being the son of Giovanni, Silver has some pretty complicated feelings about Team Rocket. Despite stealing a Pokémon himself, he doesn't like Team Rocket and will actually help the player in defeating them.
Many Pokémon fans miss rivals like Silver, ones that are clearly not your friend but are also not exactly the main antagonist either.
6 Lance (From The Manga)
Lance is commonly known as the Champion of the Elite Four and is a decent enough follow in the games and anime. In the manga though, he seeks to destroy humanity. Not only that, but he has the ability to read the feelings of Pokémon.
What makes him a likable villain is that its a refreshing take on Pokémon champions. What if one uses their power for evil instead of good? Lance's motivation is also somewhat sympathetic. Due to his ability to read the feelings of Pokémon, he cannot stand them suffering and blames humanity for it.
5 Guzma
Guzma was a welcome change in the Sun and Moon games. There is no other crime boss in the series quite like him. Rather than trying to rule the world or control a legendary Pokémon, Guzma is basically the leader of a bunch of society's outcasts. They are a pretty realistic and sobering take of those that drop out of their Pokémon journey and have no other ambitions.
The player can even discover that Guzma once wanted to be a Trial Captain and that he was once a kid just like any other young trainer with dreams of being a Pokémon master.
4 Miror B.
Miror B. is a hoot and has only graced the Gamecube games, Pokémon Colosseum and Pokémon XD. His character design is bold and fun with an afro 10 times bigger than his skull. It's also dyed to resemble a Poké Ball!
That is not all. He is into dancing and has a team entirely made up of Ludicolo. His theme music is great, and it feels as though both he and his Ludicolo are dancing to it. He's not the main antagonist of the games, but he is always a bit of a thorn in your side.
3 Mewtwo
Not all villains of Pokémon are humans (though most are). Mewtwo was certainly a special case, as he was the victim of human experimentation to the point where it saw them as enemies to Pokémon. With that kind of backstory, it is pretty difficult to not see where Mewtwo is coming from and to sympathize with him.
Even if he wasn't sympathetic, he's a Pokémon villain. That gives him an edge over other villains because he has power and abilities that make him a force to be reckoned with on a whole other level than your typical human grunt or crime boss. Also, the film that introduced him was one of the highest-grossing Pokémon titles to date.
2 James
Some fans have argued that James is a better character than Ash. He has had many moments of pure compassion for his Pokémon like with his Growlithe from childhood and when his Chimecho got sick. His personality is adorable and funny, often being quite passive and good-hearted for a villain. In fact, as a villain, he is pretty useless. Fans also love how much he bends gender norms in terms of his choice of disguises.
He is the sort of villain that puts a smile on the faces of the audience. He has also been around so long that he feels like family.
1 N
There is a lot to say about N. His storyline is pretty mature for a Pokémon character. He was found in the wilderness as a kid and (like Lance from the manga) can feel the feelings of Pokémon. From a young age, he was raised to be a symbol for an evil organization. He mistakenly believes in the organization too, as he wants Pokémon to not suffer under humans.
Other than a compelling backstory, N also has an interesting personality. He is quite smart but doesn't really know how to get along with people. His character design is also well loved by the fan community. He has also been popular enough to show up in various anime.